scPDB - 2uxx entry

Protein Data Bank Entry:

PDB ID : 2uxx

Resolution :2.740 Å

Experimental Method : X-ray

Deposition Date : 2007-03-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lysine-specific histone demethylase 1A
ID:	KDM1A_HUMAN
AC:	O60341
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	91.082
Number of residues:	65
Including
Standard Amino Acids:	64
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.250	1140.750

% Hydrophobic	% Polar
53.25	46.75
According to VolSite

Ligand :

HET Code:	FAJ
Formula:	C36H42N9O16P2
Molecular weight:	918.717 g/mol
DrugBank ID:	-
Buried Surface Area:	78.27 %
Polar Surface area:	394.42 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	9
Rings:	8
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
66.8257	64.1573	31.4556

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O8	OG	SER- 289	2.8	157.53	H-Bond (Protein Donor)	false
O8	N	SER- 289	3.15	154.18	H-Bond (Protein Donor)	false
O15	OE1	GLU- 308	2.64	156.32	H-Bond (Ligand Donor)	false
O15	OE2	GLU- 308	3.13	123.47	H-Bond (Ligand Donor)	false
O16	OE2	GLU- 308	2.57	157.71	H-Bond (Ligand Donor)	false
N7	N	ALA- 309	3.34	133.55	H-Bond (Protein Donor)	false
O16	NE	ARG- 310	3.02	122.95	H-Bond (Protein Donor)	false
C19	CG	ARG- 316	3.77	0	Hydrophobic	false
C20	CB	ARG- 316	4.44	0	Hydrophobic	false
C26	CB	ARG- 316	4.17	0	Hydrophobic	false
O10	NH2	ARG- 316	2.85	147.46	H-Bond (Protein Donor)	false
O11	NE	ARG- 316	2.81	159.72	H-Bond (Protein Donor)	false
O11	NH2	ARG- 316	3.44	129.73	H-Bond (Protein Donor)	false
O12	N	ARG- 316	3	172.35	H-Bond (Protein Donor)	false
O11	CZ	ARG- 316	3.55	0	Ionic (Protein Cationic)	false
C4	CB	ALA- 331	4.32	0	Hydrophobic	false
C23	CB	ALA- 331	4.11	0	Hydrophobic	false
C21	CB	ALA- 331	4.16	0	Hydrophobic	false
O1	N	MET- 332	2.7	169.01	H-Bond (Protein Donor)	false
O1	N	VAL- 333	2.8	172.7	H-Bond (Protein Donor)	false
N1	O	VAL- 333	2.88	162.67	H-Bond (Ligand Donor)	false
C7	CB	VAL- 333	4.33	0	Hydrophobic	false
C8	CG1	VAL- 333	4.32	0	Hydrophobic	false
C9	CG2	THR- 335	3.34	0	Hydrophobic	false
C12	CE1	PHE- 538	4.14	0	Hydrophobic	false
N8	N	VAL- 590	2.92	154.37	H-Bond (Protein Donor)	false
N9	O	VAL- 590	3.22	162.22	H-Bond (Ligand Donor)	false
C27	CG	PRO- 626	3.95	0	Hydrophobic	false
C13	CD2	LEU- 659	4.35	0	Hydrophobic	false
C17	CD1	LEU- 659	3.8	0	Hydrophobic	false
O3	NZ	LYS- 661	3.31	175.74	H-Bond (Protein Donor)	false
C17	CE2	TRP- 751	3.89	0	Hydrophobic	false
C19	CE2	TRP- 751	3.62	0	Hydrophobic	false
C30	CB	TRP- 756	3.98	0	Hydrophobic	false
C19	CB	SER- 760	3.81	0	Hydrophobic	false
C12	CZ	TYR- 761	3.99	0	Hydrophobic	false
C13	CE2	TYR- 761	4.23	0	Hydrophobic	false
C22	CD2	TYR- 761	3.72	0	Hydrophobic	false
C5	CE2	TYR- 761	3.74	0	Hydrophobic	false
C26	CB	GLU- 801	4.4	0	Hydrophobic	false
O9	N	GLU- 801	3	162.33	H-Bond (Protein Donor)	false
C10	CG2	THR- 810	3.59	0	Hydrophobic	false
O2	N	VAL- 811	3.02	149.54	H-Bond (Protein Donor)	false
C23	CG2	VAL- 811	3.95	0	Hydrophobic	false
C25	CG2	VAL- 811	4.47	0	Hydrophobic	false
C26	CB	ALA- 814	4.14	0	Hydrophobic	false
O13	O	HOH- 2003	3.21	154.68	H-Bond (Protein Donor)	false